Site Information

This site is managed at Southern Cross University on behalf of the ICGRC and in agreement with the ICGRC Steering Group. Content is prepared with editorial oversight of the ICGRC Coordinator (Prof. Graham King, SCU) who coordinates with the ICGRC community.   

The aim of the site is to provide an academically authoritative source of information. Where possible data sources are validated by reference to peer-reviewed literature. The domain is registered to Southern Cross University, Australia, and the site administration is carried out within Southern Cross Plant Science. The site is developed and maintained as part of the PhD project of Locedie Mansueto, the site's admin, under the supervision of Dr. Ramil Mauleon and Dr.Tobias Kretzschmar.

The development of this site was driven by two main goals:

  1. to host and standardize publicly available Cannabis -omics datasets to facilitate basic research and crop improvement for hemp, hempseed and medicinal cannabis.
  2. develop a plant genomics database and analysis platform focused on integrating high-throughput and multi-omics datasets.

The primary phenotypes of interest for medicinal cannabis are metabolite composition and concentration. These include cannabinoids and terpenes, which are accessible in the trichomes. We have therefore developed a model multi-omic system to study phenotype = genotype x environment x development interactions at the molecular level, as a practical use-case to develop analysis tools. For complex agronomic traits, we also provide tools to bridge between genetics and -omics studies.

Existing open-source plant genomics databases are not designed for multiple -omics analyses. These require extraction, tracking and transformation of large datasets comprising lists of molecules and samples. The multiple steps using different tools or pipelines require accurate documentation of metadata for the analysis to be replicable and the pipeline to be reusable. The system presented within this framework consist of a front-end portal using the Tripal platform, a multi-omics analysis user-interface and backend processing pipelines using Galaxy workflows. All are served by a common PostGres database through API's using open-source standards and GMOD tools.

To date there has been no open platform to organize publicly available cannabis -omics datasets. This portal aims to provide a global community-driven platform for Cannabis research, where users can contribute and curate datasets, discuss and agree on standards.

Our initial target users are the International Cannabis Genomics Research Consortium (ICGRC), whose members are leading cannabis genomics researchers. The ICGRC will work together in order to agree on commons standards that facilitate interchange and analysis of genetic, genomic and trait data. Specifically, for Cannabis, there is a need for standardization of:

  • Plant sample IDs relating to genetic resources in relation to where sourced
  • Agreement of terminology in relation to 'strain', 'cultivar', 'line', 'accession', 'plant', 'genotype'
  • Chromosome numbering and orientation used within different genome assemblies and genetic maps.
  • Genome annotation, format of gene model nomenclature and harmonization of 'reference' genomes.
  • Registries or look-up tables for genes and variants that are mapped to different reference genomes.

Ideally, the research community will move towards being able to define a pan-genome. However, to date, only a few published reference genomes have assembly and annotations of consistent quality. In the interim a more practical solution is to generate a gene catalogue that maps genome features between references. For experimental phenotypic and other 'omic datasets, existing bio-ontologies are able to be used whenever possible and this platform will encourage and facilitate their use.